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- PDB-4rrl: E129A mutant of N-terminal editing domain of threonyl-tRNA synthe... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4rrl | ||||||
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Title | E129A mutant of N-terminal editing domain of threonyl-tRNA synthetase from Aeropyrum pernix with L-Ser3AA | ||||||
![]() | Probable threonine--tRNA ligase 2 | ||||||
![]() | LIGASE / DTD-like fold / Proofreading | ||||||
Function / homology | ![]() threonyl-tRNA aminoacylation / threonine-tRNA ligase activity / aminoacyl-tRNA editing activity / tRNA binding / zinc ion binding / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Ahmad, S. / Yerabham, A.S.K. / Sankaranarayanan, R. | ||||||
![]() | ![]() Title: Specificity and catalysis hardwired at the RNA-protein interface in a translational proofreading enzyme. Authors: Ahmad, S. / Muthukumar, S. / Kuncha, S.K. / Routh, S.B. / Yerabham, A.S. / Hussain, T. / Kamarthapu, V. / Kruparani, S.P. / Sankaranarayanan, R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 42.1 KB | Display | ![]() |
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PDB format | ![]() | 28.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 718.6 KB | Display | ![]() |
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Full document | ![]() | 719.3 KB | Display | |
Data in XML | ![]() | 8.3 KB | Display | |
Data in CIF | ![]() | 10.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4rr6C ![]() 4rr7C ![]() 4rr8C ![]() 4rr9C ![]() 4rraC ![]() 4rrbC ![]() 4rrcC ![]() 4rrdC ![]() 4rrfC ![]() 4rrgC ![]() 4rrhC ![]() 4rriC ![]() 4rrjC ![]() 4rrkC ![]() 4rrmC ![]() 4rrqC ![]() 4rrrC C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 15077.378 Da / Num. of mol.: 1 / Fragment: UNP residues 1-136 / Mutation: E129A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Strain: ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1 Gene: thrS2, APE_0117.1 / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-A3S / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.37 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1M Tris HCl pH 8.5, 0.2M MgCl2, 30% PEG4000, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 23, 2012 |
Radiation | Monochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.96→25 Å / Num. all: 9189 / Num. obs: 8950 / % possible obs: 97.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.14 Å2
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Refinement step | Cycle: LAST / Resolution: 1.965→24.89 Å
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Refine LS restraints |
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